Syn and anti nucleosides

The objective of this article is to highlight aspects of the 3D structure of nucleosides, but there are links to more general descriptions of nucleosides and nucleotides available in the External Links section.

Purine Nucleosides
 Adenosine (Reset Initial scene ) is composed of an adenine bonded to a furanose by a β glycosidic bond (colored green). Observe that the adenine ring is nearly perpendicular to the furanose ring, but projecting away from the furanose (anti conformation). Without hinderance from groups on either ring the adenine ring can rotate about the glycosidic bond, and form the syn conformation. The two common purines, adenine and guanine, can rotate between the anti and syn conformations, but the anti configuration is favored. Compare the contact present between the two rings in these two spacfilling representations, anti conformation and syn conformation. Even though the anti conformation is favored with the purines the syn configuration can be formed and actually has a role in the formation of the Z-DNA, a conformation of DNA double helix.

Pyrimidine Nucleosides
View of uridine in the anti configuration, the oxygen on C-2 of uridine is projecting away from the furanose ring. View of cytidine in the syn configuration, the oxygen on C-2 is projecting toward the furanose ring. This oxygen at the C-2 position produces significant hinderance to the rotation of the pyrimidine about the glycosidic bond as shown in this scene. The oxygen doubled bonded to the C-2 invades the space of the hydrogen at C-2' and to a lesser extent the oxygen of the furanose ring. Since both pyrimidines found in DNA have an oxygen at the C-2 position, nucleosides and nucleotides of these pyrimidines only adopt the anti conformation and therefore can not be part of Z-DNA.

3D Images of Nucleotides
AMP as ball and stick ; as spacefill

UMP as ball and stick ; as spacefill

cAMP as ball and stick ; as spacefill

For additional functions of nucleotides, see: Nucleic Acids